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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ), 'gf_id' => 'HOM05D001101', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001101' ), 'data_identifier' => 'HOM05D001101', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001101', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '556', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38980' => 'bna', 'A03p39010' => 'bna', 'A07p13720' => 'bna', 'A07p31110' => 'bna', 'A07p36700' => 'bna', 'A09p40950' => 'bna', 'A09p40960' => 'bna', 'A10p23850' => 'bna', 'Aa31LG11G14610' => 'aar', 'Aa31LG4G10650' => 'aar', 'Aa31LG7G7740' => 'aar', 'Aa31LG7G7760' => 'aar', 'Aa31LG8G2070' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2420' => 'aag', 'Actinidia06033' => 'ach', 'Actinidia15029' => 'ach', 'Actinidia15030' => 'ach', 'Actinidia18809' => 'ach', 'Actinidia32588' => 'ach', 'Actinidia32589' => 'ach', 'Actinidia35207' => 'ach', 'Actinidia36074' => 'ach', 'Ah.02g129810' => 'amhyb', 'Ah.03g132590' => 'amhyb', 'Ah.06g185540' => 'amhyb', 'AL1G37630' => 'aly', 'AL1G37640' => 'aly', 'AL2G29580' => 'aly', 'AL3G27180' => 'aly', 'AL6G25660' => 'aly', 'Aqoxy1G01983' => 'aox', 'Aqoxy3G00961' => 'aox', 'Aqoxy3G03038' => 'aox', 'Aqoxy3G03039' => 'aox', 'arahy.Tifrunner.gnm1.ann1.94JZA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.97U3QM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B4IVD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BGI759' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMM3UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5PA0N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R528AV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R550IY' => 'arhy', 'AT1G23880' => 'ath', 'AT1G23890' => 'ath', 'AT1G70280' => 'ath', 'AT3G14860' => 'ath', 'AT5G14890' => 'ath', 'ATR0012G063' => 'atr', 'ATR1149G122' => 'atr', 'ATR1149G146' => 'atr', 'Atru.chr11.1996' => 'acertr', 'Atru.chr11.1997' => 'acertr', 'Atru.chr11.1998' => 'acertr', 'Atru.chr2.2065' => 'acertr', 'Atru.chr6.2184' => 'acertr', 'AUR62005350' => 'cqu', 'AUR62005351' => 'cqu', 'AUR62014002' => 'cqu', 'AUR62014004' => 'cqu', 'AUR62019596' => 'cqu', 'AUR62035943' => 'cqu', 'AUR62037563' => 'cqu', 'AUR62038813' => 'cqu', 'AUR62042413' => 'cqu', 'BcaB02g07116' => 'bca', 'BcaB02g09681' => 'bca', 'BcaB03g14787' => 'bca', 'BcaB03g15541' => 'bca', 'BcaB04g18865' => 'bca', 'BcaB04g20957' => 'bca', 'BcaB07g32363' => 'bca', 'BcaB07g32365' => 'bca', 'BcaC08g45822' => 'bca', 'BcaC08g46472' => 'bca', 'BcaC09g48454' => 'bca', 'BolC1t04914H' => 'bol', 'BolC3t16997H' => 'bol', 'BolC5t31005H' => 'bol', 'BolC5t31006H' => 'bol', 'BolC6t38734H' => 'bol', 'BolC6t39484H' => 'bol', 'BolC9t59065H' => 'bol', 'BraA01t03944Z' => 'bra', 'BraA03t13051Z' => 'bra', 'BraA07t29123Z' => 'bra', 'BraA07t30746Z' => 'bra', 'BraA07t31238Z' => 'bra', 'BraA09t39584Z' => 'bra', 'BraA09t39585Z' => 'bra', 'BraA10t44449Z' => 'bra', 'C01p49590' => 'bna', 'C03p47290' => 'bna', 'C05p23070' => 'bna', 'C05p23080' => 'bna', 'C06p36160' => 'bna', 'C06p44110' => 'bna', 'C09p62300' => 'bna', 'CAN.G205.8' => 'can', 'CAN.G205.9' => 'can', 'CAN.G206.42' => 'can', 'CAN.G375.25' => 'can', 'CANSAT01G0962' => 'cansat', 'CANSAT01G2699' => 'cansat', 'CANSAT35G0774' => 'cansat', 'CANSAT64G2323' => 'cansat', 'CARHR024280' => 'chi', 'CARHR024290' => 'chi', 'CARHR063400' => 'chi', 'CARHR089800' => 'chi', 'CARHR152430' => 'chi', 'CARHR198460' => 'chi', 'Carub.0001s2337' => 'cru', 'Carub.0001s2338' => 'cru', 'Carub.0002s1696' => 'cru', 'Carub.0003s1452' => 'cru', 'Carub.0006s1304' => 'cru', 'Ca_04209_v3' => 'car', 'Ca_04608_v3' => 'car', 'Ca_06629_v3' => 'car', 'Ca_22748_v3' => 'car', 'Ca_22749_v3' => 'car', 'Cc05_g10950' => 'ccan', 'Cc07_g02390' => 'ccan', 'Cc11_g14460' => 'ccan', 'CDE02G0595' => 'cde', 'CDE04G0011' => 'cde', 'CDE05G2472' => 'cde', 'CDE05G2845' => 'cde', 'CDE10G0134' => 'cde', 'CDE10G1169' => 'cde', 'Cfa009111' => 'cfa', 'Cfa009112' => 'cfa', 'Cfa019545' => 'cfa', 'Ciclev10014971m.g' => 'ccl', 'Ciclev10019902m.g' => 'ccl', 'Ciclev10031448m.g' => 'ccl', 'Ciclev10031709m.g' => 'ccl', 'CiPaw.03G036500' => 'cil', 'CiPaw.04G023900' => 'cil', 'CiPaw.05G147400' => 'cil', 'CiPaw.05G147500' => 'cil', 'CiPaw.06G073800' => 'cil', 'CiPaw.11G158700' => 'cil', 'CiPaw.12G112600' => 'cil', 'ClCG07G010190' => 'cla', 'ClCG09G018840' => 'cla', 'ClCG10G014400' => 'cla', 'ClCG11G017370' => 'cla', 'COL.COLO4_17509' => 'col', 'COL.COLO4_19521' => 'col', 'COL.COLO4_19522' => 'col', 'COL.COLO4_28924' => 'col', 'Cpa.g.sc140.39' => 'cpa', 'Cpa.g.sc69.5' => 'cpa', 'Cpa.g.sc69.6' => 'cpa', 'Cpa.g.sc77.33' => 'cpa', 'Cre12.g542650' => 'cre', 'CsaV3_3G042190' => 'csa', 'CsaV3_4G008130' => 'csa', 'CsaV3_4G033000' => 'csa', 'CsaV3_5G037280' => 'csa', 'CSS0003474' => 'camsi', 'CSS0010320' => 'camsi', 'CSS0017099' => 'camsi', 'CSS0019453' => 'camsi', 'CSS0021459' => 'camsi', 'CSS0026381' => 'camsi', 'CSS0031512' => 'camsi', 'CSS0032434' => 'camsi', 'CSS0035328' => 'camsi', 'CSS0045296' => 'camsi', 'DCAR_011217' => 'dca', 'DCAR_013271' => 'dca', 'DCAR_021676' => 'dca', 'DCAR_026546' => 'dca', 'DCAR_031090' => 'dca', 'Dinv00800' => 'din', 'Dinv18380' => 'din', 'Dinv24882' => 'din', 'Dinv24883' => 'din', 'Dinv31018' => 'din', 'Dinv31019' => 'din', 'Dinv31083' => 'din', 'Dinv31084' => 'din', 'Dinv33507' => 'din', 'Dinv35044' => 'din', 'Duzib147G1436' => 'dzi', 'Duzib187G1512' => 'dzi', 'Duzib213G1057' => 'dzi', 'Duzib248G0364' => 'dzi', 'Duzib251G0525' => 'dzi', 'Duzib251G0718' => 'dzi', 'Duzib268G0494' => 'dzi', 'ECA232G4298' => 'eca', 'ECA233G5872' => 'eca', 'ECA236G1330' => 'eca', 'EL10Ac2g03357' => 'bvu', 'EL10Ac6g13648' => 'bvu', 'EL10Ac6g13649' => 'bvu', 'EL10Ac6g13889' => 'bvu', 'EL10Ac9g23028' => 'bvu', 'Eucgr.B03951' => 'egr', 'Eucgr.F03283' => 'egr', 'Eucgr.J02182' => 'egr', 'Eucgr.L01895' => 'egr', 'FAN02G1158' => 'fan', 'FAN02G1561' => 'fan', 'FAN05G2631' => 'fan', 'FAN05G4804' => 'fan', 'FAN07G0286' => 'fan', 'FAN09G1428' => 'fan', 'FAN11G2831' => 'fan', 'FAN12G2180' => 'fan', 'FAN12G2904' => 'fan', 'FAN14G3585' => 'fan', 'FAN16G1275' => 'fan', 'FAN17G0312' => 'fan', 'FAN21G1665' => 'fan', 'FAN22G1327' => 'fan', 'FAN22G1364' => 'fan', 'FAN25G0535' => 'fan', 'FvH4_3g18140' => 'fve', 'FvH4_4g34810' => 'fve', 'FvH4_4g34820' => 'fve', 'FvH4_6g50490' => 'fve', 'Glyma.01G032000' => 'gma', 'Glyma.02G033400' => 'gma', 'Glyma.04G146100' => 'gma', 'Glyma.08G288800' => 'gma', 'Glyma.08G288900' => 'gma', 'Glyma.12G230967' => 'gma', 'Glyma.12G231033' => 'gma', 'Glyma.13G268500' => 'gma', 'Glyma.18G135751' => 'gma', 'Glyma.18G135800' => 'gma', 'Glyma.19G011000' => 'gma', 'Gohir.A04G043400' => 'ghi', 'Gohir.A04G134900' => 'ghi', 'Gohir.A05G318200' => 'ghi', 'Gohir.A07G219100' => 'ghi', 'Gohir.D04G178100' => 'ghi', 'Gohir.D05G320500' => 'ghi', 'Gohir.D05G340200' => 'ghi', 'Gohir.D07G226100' => 'ghi', 'Gorai.001G260900' => 'gra', 'Gorai.009G343600' => 'gra', 'Gorai.009G366600' => 'gra', 'Gorai.012G171100' => 'gra', 'GSVIVG01014170001' => 'vvi', 'GSVIVG01020207001' => 'vvi', 'GSVIVG01020208001' => 'vvi', 'GSVIVG01032504001' => 'vvi', 'HanXRQChr04g0103691' => 'han', 'HanXRQChr04g0108531' => 'han', 'HanXRQChr05g0153131' => 'han', 'HanXRQChr08g0208881' => 'han', 'HanXRQChr08g0220581' => 'han', 'HanXRQChr09g0265951' => 'han', 'HanXRQChr12g0371421' => 'han', 'Haze_09306' => 'cav', 'Haze_09307' => 'cav', 'Haze_12149' => 'cav', 'Haze_12150' => 'cav', 'Haze_14655' => 'cav', 'Hma1.2p1_0160F.1_g070690' => 'hma', 'Hma1.2p1_0697F.1_g204810' => 'hma', 'Hma1.2p1_0867F.1_g230370' => 'hma', 'Hma1.2p1_0867F.1_g230380' => 'hma', 'Hma1.2p1_1650F.1_g295650' => 'hma', 'Hma1.2p1_1872F.1_g306120' => 'hma', 'HPP92_019253' => 'vpl', 'HPP92_019255' => 'vpl', 'HPP92_019922' => 'vpl', 'HPP92_020064' => 'vpl', 'HPP92_020070' => 'vpl', 'Hund05974' => 'sun', 'Hund05975' => 'sun', 'Hund10538' => 'sun', 'Hund12472' => 'sun', 'Hund25336' => 'sun', 'Lalb_Chr03g0031231' => 'lal', 'Lalb_Chr05g0217011' => 'lal', 'Lalb_Chr09g0326421' => 'lal', 'Lalb_Chr09g0335061' => 'lal', 'Lalb_Chr16g0382351' => 'lal', 'Lalb_Chr16g0392451' => 'lal', 'Lalb_Chr20g0109211' => 'lal', 'Lalb_Chr21g0319371' => 'lal', 'Lj2g0009470' => 'lja', 'Lj2g0019927' => 'lja', 'Lj2g0022927' => 'lja', 'Lj3C23T3' => 'lonja', 'Lj3C9T2' => 'lonja', 'Lj3g0007321' => 'lja', 'Lj3g0027156' => 'lja', 'Lj4g0015107' => 'lja', 'Lj4g0015491' => 'lja', 'Lj6A803T82' => 'lonja', 'Lj6C803T14' => 'lonja', 'Lj7C589T17' => 'lonja', 'Lj8A147G49' => 'lonja', 'Lsat_1_v5_gn_0_12400' => 'lsa', 'Lsat_1_v5_gn_3_64401' => 'lsa', 'Lsat_1_v5_gn_4_181520' => 'lsa', 'Lsat_1_v5_gn_4_6680' => 'lsa', 'Lsat_1_v5_gn_7_102241' => 'lsa', 'Lsat_1_v5_gn_7_99620' => 'lsa', 'Lsat_1_v5_gn_8_159121' => 'lsa', 'Manes.01G198700' => 'mes', 'Manes.03G099900' => 'mes', 'Manes.05G088000' => 'mes', 'Manes.05G088100' => 'mes', 'Manes.05G088200' => 'mes', 'Manes.05G088250' => 'mes', 'Manes.15G096600' => 'mes', 'Manes.15G181160' => 'mes', 'Manes.17G123300' => 'mes', 'Mapoly0071s0036' => 'mpo', 'MBI06_g16699_MAGBIO' => 'mbi', 'MBI07_g00455_MAGBIO' => 'mbi', 'MBI14_g17549_MAGBIO' => 'mbi', 'MBI15_g31107_MAGBIO' => 'mbi', 'MBI15_g31108_MAGBIO' => 'mbi', 'MBI16_g37124_MAGBIO' => 'mbi', 'MD09G1036000' => 'mdo', 'MD11G1265700' => 'mdo', 'MD13G1089400' => 'mdo', 'MD13G1089500' => 'mdo', 'MD16G1089600' => 'mdo', 'MD16G1089700' => 'mdo', 'MD17G1037600' => 'mdo', 'Medtr2g075860' => 'mtr', 'Medtr5g034550' => 'mtr', 'Medtr5g034750' => 'mtr', 'Medtr6g007720' => 'mtr', 'Medtr8g058280' => 'mtr', 'Medtr8g058310' => 'mtr', 'Medtr8g058630' => 'mtr', 'Medtr8g063700' => 'mtr', 'Medtr8g063760' => 'mtr', 'MELO3C009940.2' => 'cme', 'MELO3C016123.2' => 'cme', 'MELO3C021532.2' => 'cme', 'MELO3C025648.2' => 'cme', 'MELO3C030675.2' => 'cme', 'Migut.H00139' => 'egut', 'Migut.L01428' => 'egut', 'Migut.L01429' => 'egut', 'Migut.M00709' => 'egut', 'MSTRG.14970' => 'ama', 'MSTRG.24001' => 'ama', 'MSTRG.6684' => 'ama', 'MSTRG.7883' => 'ama', 'Nitab4.5_0000052g0300' => 'nta', 'Nitab4.5_0000052g0350' => 'nta', 'Nitab4.5_0000052g0370' => 'nta', 'Nitab4.5_0000788g0050' => 'nta', 'Nitab4.5_0001952g0060' => 'nta', 'Nitab4.5_0007879g0050' => 'nta', 'Nitab4.5_0008887g0010' => 'nta', 'Nitab4.5_0008887g0040' => 'nta', 'Nitab4.5_0016997g0010' => 'nta', 'Nn3g21084' => 'nnu', 'Nn4g22832' => 'nnu', 'Nn4g22834' => 'nnu', 'Nn4g22835' => 'nnu', 'Nn4g22843' => 'nnu', 'Nn6g34473' => 'nnu', 'Oeu001671.1' => 'oeu', 'Oeu025436.1' => 'oeu', 'Oeu027460.1' => 'oeu', 'Oeu028909.1' => 'oeu', 'Oeu031024.1' => 'oeu', 'Os02g0234200' => 'osa', 'Os02g0730400' => 'osa', 'Os06g0269300' => 'osa', 'Os08g0414600' => 'osa', 'Peaxi162Scf00111g01465' => 'pax', 'Peaxi162Scf00129g00940' => 'pax', 'Peaxi162Scf00421g00119' => 'pax', 'Peaxi162Scf00421g00121' => 'pax', 'PGR031G1547' => 'pgr', 'PGR083G2325' => 'pgr', 'PGR102G2733' => 'pgr', 'PGR119G1830' => 'pgr', 'PGSC0003DMG400000502' => 'stu', 'PGSC0003DMG400004115' => 'stu', 'PGSC0003DMG400004127' => 'stu', 'PGSC0003DMG400007097' => 'stu', 'Phvul.002G072500' => 'pvu', 'Phvul.003G053100' => 'pvu', 'Phvul.003G053200' => 'pvu', 'Phvul.004G018200' => 'pvu', 'Phvul.005G081000' => 'pvu', 'Phvul.011G166300' => 'pvu', 'Potri.001G387500' => 'ptr', 'Potri.004G087300' => 'ptr', 'Potri.008G147700' => 'ptr', 'Potri.009G072933' => 'ptr', 'Potri.010G094200' => 'ptr', 'Potri.011G107800' => 'ptr', 'Potri.016G092200' => 'ptr', 'Potri.017G129500' => 'ptr', 'Pp3c13_9240' => 'ppa', 'Pp3s30_450' => 'ppa', 'Prupe.1G256300' => 'ppe', 'Prupe.1G256400' => 'ppe', 'Prupe.3G281800' => 'ppe', 'Prupe.4G160200' => 'ppe', 'Psat0s2485g0080' => 'psa', 'Psat1g059680' => 'psa', 'Psat2g092920' => 'psa', 'Psat2g105520' => 'psa', 'Psat3g144680' => 'psa', 'Psat4g125040' => 'psa', 'Psat4g127640' => 'psa', 'PSO017G3792' => 'pso', 'PSO063G2075' => 'pso', 'PSO080G0001' => 'pso', 'PSO339G1702' => 'pso', 'PSO384G1315' => 'pso', 'PSO541G3246' => 'pso', 'PSO675G9353' => 'pso', 'PSO832G3645' => 'pso', 'QL02p077025' => 'qlo', 'QL03p061860' => 'qlo', 'QL03p061872' => 'qlo', 'QL04p008927' => 'qlo', 'QL05p049469' => 'qlo', 'QL06p020760' => 'qlo', 'QL08p025698' => 'qlo', 'QL08p027176' => 'qlo', 'RcHm_v2.0_Chr2g0093451' => 'rch', 'RcHm_v2.0_Chr2g0170891' => 'rch', 'RcHm_v2.0_Chr2g0175351' => 'rch', 'RcHm_v2.0_Chr4g0444151' => 'rch', 'RcHm_v2.0_Chr4g0444161' => 'rch', 'RcHm_v2.0_Chr5g0006981' => 'rch', 'RcHm_v2.0_Chr5g0030571' => 'rch', 'Rhsim06G0210100' => 'rsi', 'Rhsim10G0024200' => 'rsi', 'Rhsim12G0122000' => 'rsi', 'Rhsim12G0122100' => 'rsi', 'Sabra04G0058200' => 'sbr', 'Sabra08G0112300' => 'sbr', 'Sabra10G0066400' => 'sbr', 'Sabra11G0095800' => 'sbr', 'Sabra16G0097800' => 'sbr', 'Sabra16G0254800' => 'sbr', 'SalBow1G0277' => 'sbo', 'SalBow1G6953' => 'sbo', 'SalBow2G1519' => 'sbo', 'SalBow2G1559' => 'sbo', 'SalBow2G3253' => 'sbo', 'SalBow8G2079' => 'sbo', 'Sc03g0010600' => 'sci', 'Sc04g0009020' => 'sci', 'Sc04g0009030' => 'sci', 'Sc09g0006930' => 'sci', 'Sc11g0001270' => 'sci', 'Sed0014809' => 'sed', 'Sed0023173' => 'sed', 'Sed0025023' => 'sed', 'Sed0027020' => 'sed', 'Sed0027959' => 'sed', 'SEGI_12056' => 'sgi', 'SEGI_14575' => 'sgi', 'SEGI_15311' => 'sgi', 'SEGI_15421' => 'sgi', 'SGA_v2.0_scaffold135G34853' => 'sas', 'SGA_v2.0_scaffold165G38262' => 'sas', 'SGA_v2.0_scaffold165G38263' => 'sas', 'SGA_v2.0_scaffold73G24397' => 'sas', 'SHI24753' => 'shi', 'SHI48682' => 'shi', 'SMO170G0086' => 'smo', 'SMO180G0010' => 'smo', 'SMO180G0011' => 'smo', 'SMO184G0014' => 'smo', 'SMO340G0286' => 'smo', 'SMO340G0298' => 'smo', 'Solyc02g087010.2' => 'sly', 'Solyc05g005760.4' => 'sly', 'Solyc05g005770.3' => 'sly', 'Solyc06g048720.1' => 'sly', 'Solyc07g062300.3' => 'sly', 'Solyc10g018280.1' => 'sly', 'Solyc10g018290.2' => 'sly', 'Sopen02g031780' => 'spe', 'Sopen05g001760' => 'spe', 'Sopen05g001770' => 'spe', 'Sopen07g030570' => 'spe', 'Sopen12g028040' => 'spe', 'Sp1g21230' => 'spa', 'Sp1g21240' => 'spa', 'Sp3g13070' => 'spa', 'Sp5g25390' => 'spa', 'Sp6g29160' => 'spa', 'Sp6g29190' => 'spa', 'TAR371G0907' => 'tar', 'TAR374G0612' => 'tar', 'TAR623G1018' => 'tar', 'TAR626G0991' => 'tar', 'TAR627G0318' => 'tar', 'TAR629G0388' => 'tar', 'TAR629G2171' => 'tar', 'TAR629G2731' => 'tar', 'THA.LOC104802407' => 'tha', 'THA.LOC104808927' => 'tha', 'THA.LOC104815575' => 'tha', 'THA.LOC104822132' => 'tha', 'THA.LOC104822133' => 'tha', 'Thecc.02G246000' => 'tca', 'Thecc.02G246100' => 'tca', 'Thecc.04G006900' => 'tca', 'Thecc.07G126600' => 'tca', 'Thhalv10007420m.g' => 'esa', 'Thhalv10007807m.g' => 'esa', 'Thhalv10012875m.g' => 'esa', 'Thhalv10018442m.g' => 'esa', 'Thhalv10020396m.g' => 'esa', 'TPR.G16052' => 'tpr', 'TPR.G20390' => 'tpr', 'TPR.G21867' => 'tpr', 'TPR.G23076' => 'tpr', 'TPR.G2311' => 'tpr', 'TPR.G29174' => 'tpr', 'TPR.G31967' => 'tpr', 'TWI12G1205' => 'twi', 'TWI18G1371' => 'twi', 'TWI38G2134' => 'twi', 'TWI39G0632' => 'twi', 'TWI75G0662' => 'twi', 'unitig_22.g6469' => 'ugi', 'unitig_22.g6931' => 'ugi', 'unitig_699.g19931' => 'ugi', 'unitig_746.g26570' => 'ugi', 'unitig_747.g21588' => 'ugi', 'vmacro05810' => 'vma', 'vmacro11953' => 'vma', 'vmacro16266' => 'vma', 'vmacro16267' => 'vma', 'VMungo0251G1292' => 'vmu', 'VMungo0251G1563' => 'vmu', 'VMungo0464G2188' => 'vmu', 'VMungo1080G1788' => 'vmu', 'VMungo1127G0294' => 'vmu', 'VMungo1215G1219' => 'vmu', 'Zm00001eb042340' => 'zma', 'Zm00001eb111460' => 'zma', 'Zm00001eb189950' => 'zma', 'Zm00001eb239070' => 'zma', 'Zm00001eb253510' => 'zma', 'Zm00001eb280410' => 'zma', 'Zm00001eb302130' => 'zma', 'Zm00001eb380240' => 'zma' ) $gf_id = 'HOM05D001101' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001101' ) $data_identifier = 'HOM05D001101' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 11, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 7, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 8, 'ppa' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 8, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 6, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb380240' $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